Extract applications #288
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Extract applications #288
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…eters of applications in a simulation - Add a function `exportParametersToXLS` to write parameter information into an excel file that can be loaded in MoBi or R - Add a function `writeExcel` that is a wrapper for creating a directory (if not present) and writing to excel file
…tract-applications
Codecov Report
@@ Coverage Diff @@
## develop #288 +/- ##
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+ Coverage 58.91% 60.71% +1.79%
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Files 23 23
Lines 1110 1148 +38
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+ Hits 654 697 +43
+ Misses 456 451 -5
Continue to review full report at Codecov.
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IndrajeetPatil
suggested changes
Jul 28, 2022
| moleculeNames <- moleculeNames %||% simulation$allFloatingMoleculeNames() | ||
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| # Returns an object of class `Application` for each administration event | ||
| applications <- unlist(lapply(moleculeNames, \(x)simulation$allApplicationsFor(x)), use.names = FALSE) |
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We support R versions > 3.6, and so the anonymous function syntax (\()) can't be used with these older versions of R.
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Why not support at least 4.1? I think this is even written somewhere on BlueSpice that R 4.2 should be used.
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Fine by me.
But then you should also bump the needed R version in the DESCRIPTION file.
R/utilities-simulation.R
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| #' @param moleculeNames Names of the molecules for which administrations the | ||
| #' parameters will be returned. If `NUll`(default), applications for all |
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Something is missing in this first sentence.
administrations of the parameters?
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The parameters of the applications of the molecules... Don't really know how to properly phrase it.
R/utilities-parameters.R
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| # has been provided | ||
| data <- list(output) | ||
| if (!is.null(sheet)) { | ||
| validateIsOfLength(sheet, 1) |
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All validations should happen early on to avoid failing after expensive computations.
You can move this to the top with the addition of , nullAllowed = TRUE.
Co-authored-by: Indrajeet Patil <[email protected]>
Co-authored-by: Indrajeet Patil <[email protected]>
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Looking good. One last thing: Can you please also make a note of all these changes in NEWS.md? Including the change in needed R version. |
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NEWS updated |
IndrajeetPatil
approved these changes
Jul 28, 2022
PavelBal
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Sep 26, 2022
* Create V4 (#255) * - Update data-handling vignette - Function `loadObservedData()` requires a `ProjectConfiguration` instead of a `ScenarioConfiguration`. * Remove unused vignettes * Update AppVeyor to R4.2.0 * Increment version to v4.0.0 * Cleanup for v4 * Update website * Update reference index * Removed steady-state function and using ospsuite.parameteridentification (#261) * Removed steady-state function and using ospsuite.parameteridentification * Update NEWS.md Co-authored-by: Indrajeet Patil <[email protected]> * Removed unused message * Update documentation * Update appveyor.yml * Fix examples Co-authored-by: Indrajeet Patil <[email protected]> * Add functions to create plotting-related configs (#265) - [x] Closes #262 - [x] Closes #263 - [x] Closes #264 - [x] Closes #225 - [x] docs and NEWS - [x] tests * Following guidelines for internal function names (#266) * Added simulationRunOptions parameter (#268) * Added simulationRunOptions parameter * Remove `hash` from imports Adds `stringr` and `labeling` to imports Remove "return" from an empty switch statement Missing documented arguments * Update to roxygen2 7.2.1 (#273) * Update to roxygen2 7.2.1 * .rd files * Update exportSteadyStateToXLS.Rd * Don't write to sheets when there is no data (#274) Closes #272 * SensitivityAnalysis - use "by path" methods (#271) * Use unlist * Assign condition to a variable * Skipping tests that rely on PK-Sim * fix `createEsqlabsPlotConfiguration()` Co-authored-by: Indrajeet Patil <[email protected]> * Follow coding convention for source code filenames (#275) * remove empty section from reference page * Fix failing sensitivity-calculation after ospsuite update (#278) * Fix failing sensitivity-calculation after ospsuite update * Update rd * Add tests for utilities (#280) * Add tests for file utilities * snapshot paths have changed? * skip for now * try * problematic test? * Update test-utilities-file.R * Update test-utilities-file.R * Update test-utilities-file.R * Test for `compareWithNA()` * rudimentary test for `ScenarioConfiguration` * Don't skip tests on CI anymore (#283) * Update README (#282) * Update README Closes #281 * Update README.md * Tests for color utilities and global settings (#285) * Tests for color utilities * tests for global settings * Use functions for error messages * Additional tests for utilities (#287) * Additional tests for utilities * test for `compareSimulationParameters()` * tweak tests for settings * Test for `sampleRandomValue()` * Address review comments * remove `expect_s3_class()` for R6 * Extract applications (#288) * - Add a function `getAllApplicationParameters` that returns all parameters of applications in a simulation - Add a function `exportParametersToXLS` to write parameter information into an excel file that can be loaded in MoBi or R - Add a function `writeExcel` that is a wrapper for creating a directory (if not present) and writing to excel file * Update documentation * Update R/utilities-simulation.R Co-authored-by: Indrajeet Patil <[email protected]> * Update R/utilities-parameters.R Co-authored-by: Indrajeet Patil <[email protected]> * Address review comments * Update required R version * Update NEWS Co-authored-by: Indrajeet Patil <[email protected]> * Tests for shiny apps (#290) * Get rid of a few lints (#291) * also not used * - Add default project configuration file (#293) - Fix documentation for the simulationTime argument of ScenarioConfiguration - Fix example for setParameterValuesByPathWithCondition - If simulation time is not defined in the ScenarioConfiguration, use output time schema from the simulation * More tests for utilities (#294) * More tests for utilities * use github version * skip for now * Test for `executeInParallel()` * Try shipping binary * Revert "Try shipping binary" This reverts commit 72dda5d. * Update documentation (#298) * More tests for scenario config (#296) * more tests for scenario config * to shut up codecov * Get rid of `.getNetHashCode()` Closes #297 * Added example project * Add logo for the package (#299) Stickers are big in the R community, and a good way to market ourselves at conferences and meetings. Print them, and distribute them, so that people can put them on their laptops. cc @StephanSchaller * - Remove unused test files - Styler * Delete modeling_environment.R unneeded for the esqlabsR purposes * Documenting data handling and running simulations (#301) * Updated the introduction part of the vignette * Data handling vignette * Vignette on running simulations * Propagated vignette updates to the /docs folder * Updated links to the scenario file to avoid duplicated files * style * style changes to vignettes/data-handling.Rmd Co-authored-by: Indrajeet Patil <[email protected]> * Restored _snaps files that were mistakenly removed * wording in introduction Co-authored-by: Pavel Balazki <[email protected]> * link to aciclovir model Co-authored-by: Pavel Balazki <[email protected]> * Removed function reference, moved installation and contribution to README.md only * style changes README.md Co-authored-by: Indrajeet Patil <[email protected]> * Removed auto-generated testthat file * Update vignettes/introduction-esqlabsr.Rmd * Changes to data-handling.Rmd Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: Pavel Balazki <[email protected]> * Better explanation of the configuration Excel files * Restructuring of existing documentation, a clear description of no-code approach * Run tests for Shiny apps (#303) * Simulations vignette with references to all configuration files and first lines of output * Fixed link to the Scenarios.xlsx file * Visualization vignette * Sensitivity vignette * Add getMoleculeNameFromQuantity() (#307) * Add getMoleculeNameFromQuantity() * Apply suggestions from code review Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: Indrajeet Patil <[email protected]> * Changed plot sizes * Added troubleshooting sections * Apply suggestions from code review style changes Co-authored-by: Indrajeet Patil <[email protected]> * Apply suggestions from code review style changes Co-authored-by: Indrajeet Patil <[email protected]> * Renamed chunks to follow style guide * Added time profiles to sensitivity analysis * Update vignettes/sensitivity-analysis.Rmd * Added link to time profiles * Updated the HTML docs to match the RMD docs (#309) * Updated the HTML docs to match the RMD docs * correct typos Co-authored-by: Indrajeet Patil <[email protected]> * Suggestions for vignettes (#315) Co-authored-by: Johanna Eitel <[email protected]> * Fixes initializeSimulation() when additionalParams is empty but not NULL #313 (#314) * Added script for installation * - List for packages that will be installed from CRAN - Add "purr" explicitly to be installed from CRAN * - Add jsonlite to be installed * - Change defaults for `updatePackages` argument to `FALSE` - Change defaults for `developerVersion` to `TRUE` - Remove redundant test for PK-Sim connection * Add vignette for shiny apps (#316) * Add vignette for shiny apps * Added header, minor style changes * Add ShinyApp link to the introduction Some minor changes to the vignette Co-authored-by: Johanna Eitel <[email protected]> Co-authored-by: Sergei Vavilov <[email protected]> Co-authored-by: Pavel Balazki <[email protected]> * Update website (#327) * - Remove RData - Update readme * Update docs Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: Johanna Eitel <[email protected]> Co-authored-by: Sergei Vavilov <[email protected]> Co-authored-by: Johanna Eitel <[email protected]>
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getAllApplicationParametersthat returns all parameters of applications in a simulationexportParametersToXLSto write parameter information into an excel file that can be loaded in MoBi or RwriteExcelthat is a wrapper for creating a directory (if not present) and writing to excel file